Mercurial > repos > devteam > emboss_5
comparison emboss_pepinfo.xml @ 11:0e2484b6829b draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/emboss_5 commit b583bbeb8fc90cd4b1e987a56982e7cf4aed1a68
author | iuc |
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date | Mon, 30 Jan 2017 13:27:40 -0500 |
parents | 9b98d3d903c6 |
children | 27c43fb015f0 |
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10:9b98d3d903c6 | 11:0e2484b6829b |
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1 <tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0"> | 1 <tool id="EMBOSS: pepinfo69" name="pepinfo" version="5.0.0.1"> |
2 <!-- puts file info in output files --> | 2 <!-- puts file info in output files --> |
3 <description>Plots simple amino acid properties in parallel</description> | 3 <description>Plots simple amino acid properties in parallel</description> |
4 <requirements><requirement type="package" version="5.0.0">emboss</requirement></requirements> | 4 <macros> |
5 <command interpreter="perl">emboss_single_outputfile_wrapper.pl pepinfo -sequence $input1 -outfile $out_file1 -goutfile $out_file2 -graph png -hwindow $hwindow $plot_type -auto</command> | 5 <import>macros.xml</import> |
6 </macros> | |
7 <expand macro="requirements" /> | |
8 <command>perl '$__tool_directory__/emboss_single_outputfile_wrapper.pl' pepinfo -sequence '$input1' -outfile '$out_file1' -goutfile '$out_file2' -graph png -hwindow $hwindow $plot_type -auto</command> | |
6 <inputs> | 9 <inputs> |
7 <param format="data" name="input1" type="data"> | 10 <param name="input1" type="data" format="data" label="Sequence" /> |
8 <label>Sequence</label> | 11 <param name="hwindow" type="integer" value="9" label="Window size for hydropathy averaging" /> |
9 </param> | 12 <param name="plot_type" type="select" label="Choose a plot type"> |
10 <param name="hwindow" type="text" value="9"> | |
11 <label>Window size for hydropathy averaging</label> | |
12 </param> | |
13 <param name="plot_type" type="select"> | |
14 <label>Choose a plot type</label> | |
15 <option value="-generalplot yes -hydropathyplot no">Histogram of general properties</option> | 13 <option value="-generalplot yes -hydropathyplot no">Histogram of general properties</option> |
16 <option value="-generalplot no -hydropathyplot yes">Graphs of hydropathy</option> | 14 <option value="-generalplot no -hydropathyplot yes">Graphs of hydropathy</option> |
17 </param> | 15 </param> |
18 </inputs> | 16 </inputs> |
19 <outputs> | 17 <outputs> |
20 <data format="pepinfo" name="out_file1" /> | 18 <data name="out_file1" format="pepinfo" /> |
21 <data format="png" name="out_file2" /> | 19 <data name="out_file2" format="png" /> |
22 </outputs> | 20 </outputs> |
23 <help> | 21 <help> |
24 You can view the original documentation here_. | 22 You can view the original documentation here_. |
25 | |
26 .. _here: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/pepinfo.html | |
27 | 23 |
28 ------ | 24 .. _here: http://galaxy-iuc.github.io/emboss-5.0-docs/pepinfo.html |
29 | |
30 **Citation** | |
31 | |
32 For the underlying tool, please cite `Rice P, Longden I, Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet. 2000 Jun;16(6):276-7. <http://www.ncbi.nlm.nih.gov/pubmed/10827456>`_ | |
33 | |
34 If you use this tool in Galaxy, please cite `Blankenberg D, Taylor J, Schenck I, He J, Zhang Y, Ghent M, Veeraraghavan N, Albert I, Miller W, Makova KD, Hardison RC, Nekrutenko A. A framework for collaborative analysis of ENCODE data: making large-scale analyses biologist-friendly. Genome Res. 2007 Jun;17(6):960-4. <http://www.ncbi.nlm.nih.gov/pubmed/17568012>`_ | |
35 </help> | 25 </help> |
26 <expand macro="citations" /> | |
36 </tool> | 27 </tool> |